The present invention overcomes the limitations of the prior art by providing a method and system for compensating for the actuator resonances that may be higher than the Nyquist frequency. In an exemplary embodiment, a controller generates a control signal that is input into a voice coil motor and causes an actuator to move to a particular position on the storage disk. An actuator model is also coupled to the output of the controller. The actuator model is used to estimate the response of the actuator when a signal is input into the voice coil motor. If some voltage is induced in the voice coil motor by an external vibration or resonance of the actuator, then the voltage output by the actuator will not be equal to the estimated voltage output by the actuator model. The difference of the estimated voltage and the actual voltage output the actuator is input into a resonance controller. The resonance controller then generates a compensation signal that is combined with the control signal to compensate for any actuator resonances.